htsjdk.samtools

Enum SamPairUtil.PairOrientation

java.lang.Object

java.lang.Enum<SamPairUtil.PairOrientation>

htsjdk.samtools.SamPairUtil.PairOrientation

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<SamPairUtil.PairOrientation>

Enclosing class:

SamPairUtil

public static enum SamPairUtil.PairOrientation
extends java.lang.Enum<SamPairUtil.PairOrientation>

The possible orientations of paired reads. F = mapped to forward strand R = mapped to reverse strand FR means the read that's mapped to the forward strand comes before the read mapped to the reverse strand when their 5'-end coordinates are compared.

Enum Constant Summary

Enum Constants

Enum Constant and Description
FR
RF
TANDEM

Method Summary

Methods

Modifier and Type	Method and Description
static SamPairUtil.PairOrientation	valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static SamPairUtil.PairOrientation[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

FR

public static final SamPairUtil.PairOrientation FR

RF

public static final SamPairUtil.PairOrientation RF

TANDEM

public static final SamPairUtil.PairOrientation TANDEM

Method Detail

values

public static SamPairUtil.PairOrientation[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (SamPairUtil.PairOrientation c : SamPairUtil.PairOrientation.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static SamPairUtil.PairOrientation valueOf(java.lang.String name)

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

java.lang.IllegalArgumentException - if this enum type has no constant with the specified name

java.lang.NullPointerException - if the argument is null